<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>Merges bins from a Hi-C matrix</description>
    <macros>
        <token name="@BINARY@">hicMergeMatrixBins</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        hicMergeMatrixBins
            --matrix '$matrix_h5_cooler'
            --numBins $numBins
            $runningWindow
            --outFileName matrix.$outputFormat
        && mv matrix.$outputFormat matrix

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />

        <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
        <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
        <param name='outputFormat' type='select' label="Output file format">
            <option value='h5' selected='true'>HiCExplorer format</option>
            <option value="cool">cool</option>
        </param>
    </inputs>
    <outputs>
        <data name="outFileName" from_work_dir="matrix" format="h5">
              <change_format>
                <when input="outputFormat" value="cool" format="cool" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
            <param name="numBins" value="5" />
            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
        </test>
    </tests>
    <help><![CDATA[

Change matrix resolution
========================

``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb 
contact matrix a 1000 kb one:

Number of bins to merge = 10

100 kb * 10 = 1000 kb = 1 Mb

This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is
to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but 
to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it 
difficult to interpret, especially if the read depth of the Hi-C data is not high.

Input
-----

Parameters
__________
- contact matrix to change the resolution on
- Number of bins to merge
- running window

Output
------

A contact matrix with the resolution ``original resolution * number of bins``.

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]></help>
    <expand macro="citations" />
</tool>